posCalc: FUNCTION posCalc and fillMarkInfo

In idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

Description

calculates position of marks in fraction of (%) chromosome units (0-1)

Usage

posCalc(
  dfMarkPos,
  listOfdfChromSize,
  bToRemove = "",
  markDistType = "beg",
  origin = "b",
  showBandList = FALSE,
  result = "tibble"
)

fillMarkInfo2(dfMarkPos, dfChrSize)

fillMarkInfo(dfMarkPos, dfChrSize, markDistType = "beg", origin = "b")

Arguments

dfMarkPos	data.frame of marks' position
listOfdfChromSize	list (for posCalc) or data.frames of chr. sizes.
bToRemove,	character, bands to remove from calc. of pos.
markDistType	markDistType character, if "cen" = the distance you provided in data.frame (dfMarkPos) column markDistCen or markPos is to the center of the mark, if "beg" = the distance you provided is to the beginning of the mark (Default)
origin,	character, For non-monocentric chr. (for holocentrics only) Use "b" (default) if distance to mark in ("markPos" column in "dfMarkPos") data.frame measured from bottom of chromosome, use "t" for distance to mark from top of chr.
showBandList,	boolean, show row of all bands in tibble, see "result"
result	character, use "tibble" to get results in tibble, "data.frame", or other string results in a list
dfChrSize	data.frame of chr. sizes

Value

list, tibble

data.frame of marks

data.frame of marks

Examples

load(system.file("shinyApps", "iBoard/www/rda/monoholoCS.rda", package = "idiogramFISH") )
load(system.file("shinyApps", "iBoard/www/rda/monoholoMarks.rda", package = "idiogramFISH") )
monoholoMarks2 <- fillMarkInfo(monoholoMarks,monoholoCS)
posCalc(monoholoMarks2,monoholoCS, result="data.frame")

idiogramFISH documentation built on Sept. 30, 2021, 5:07 p.m.